1XQL

Effect of a Y265F Mutant on the Transamination Based Cycloserine Inactivation of Alanine Racemase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

Starting Model: experimental
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This is version 1.7 of the entry. See complete history


Literature

Effect of a Y265F Mutant on the Transamination-Based Cycloserine Inactivation of Alanine Racemase

Fenn, T.D.Holyoak, T.Stamper, G.F.Ringe, D.

(2005) Biochemistry 44: 5317-5327

  • DOI: https://doi.org/10.1021/bi047842l
  • Primary Citation of Related Structures:  
    1XQK, 1XQL

  • PubMed Abstract: 

    The requirement for d-alanine in the peptidoglycan layer of bacterial cell walls is fulfilled in part by alanine racemase (EC 5.1.1.1), a pyridoxal 5'-phosphate (PLP)-assisted enzyme. The enzyme utilizes two antiparallel bases focused at the C(alpha) position and oriented perpendicular to the PLP ring to facilitate the equilibration of alanine enantiomers. Understanding how this two-base system is utilized and controlled to yield reaction specificity is therefore a potential means for designing antibiotics. Cycloserine is a known alanine racemase suicide substrate, although its mechanism of inactivation is based on transaminase chemistry. Here we characterize the effects of a Y265F mutant (Tyr265 acts as the catalytic base in the l-isomer case) of Bacillus stearothermophilus alanine racemase on cycloserine inactivation. The Y265F mutant reduces racemization activity 1600-fold [Watanabe, A., Yoshimura, T., Mikami, B., and Esaki, N. (1999) J. Biochem. 126, 781-786] and only leads to formation of the isoxazole end product (the result of the transaminase pathway) in the case of d-cycloserine, in contrast to results obtained using the wild-type enzyme. l-Cycloserine, on the other hand, utilizes a number of alternative pathways in the absence of Y265, emphasizing the importance of Y265 in both the inactivation and racemization pathway. In combination with the kinetics of inactivation, these results suggest roles for each of the two catalytic bases in racemization and inactivation, as well as the importance of Y265 in "steering" the chemistry to favor one pathway over another.


  • Organizational Affiliation

    Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alanine racemase
A, B
388Geobacillus stearothermophilusMutation(s): 2 
Gene Names: alrdal
EC: 5.1.1.1
UniProt
Find proteins for P10724 (Geobacillus stearothermophilus)
Explore P10724 
Go to UniProtKB:  P10724
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10724
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PMH
Query on PMH

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
(5-HYDROXY-4-{[(3-HYDROXYISOXAZOL-4-YL)AMINO]METHYL}-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE
C11 H14 N3 O7 P
PXWFNGNWQUPGPJ-UHFFFAOYSA-N
PMP
Query on PMP

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
PLP
Query on PLP

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
4AX
Query on 4AX

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
(R)-4-AMINO-ISOXAZOLIDIN-3-ONE
C3 H6 N2 O2
DYDCUQKUCUHJBH-UWTATZPHSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, B
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.776α = 90
b = 89.795β = 90
c = 85.177γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2018-05-02
    Changes: Data collection
  • Version 1.5: 2021-10-20
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.6: 2023-08-23
    Changes: Data collection, Refinement description
  • Version 1.7: 2023-11-15
    Changes: Data collection